Database of human brain images derived from a realistic phantom and generated using a sophisticated MRI simulator. Custom simulations may be generated to match a user's selected parameters. The goal is to aid validation of computer-aided quantitative analysis of medical image data. The SBD contains a set of realistic MRI data volumes produced by an MRI simulator. These data can be used by the neuroimaging community to evaluate the performance of various image analysis methods in a setting where the truth is known. The SBD contains simulated brain MRI data based on two anatomical models: normal and multiple sclerosis (MS). For both of these, full 3-dimensional data volumes have been simulated using three sequences (T1-, T2-, and proton-density- (PD-) weighted) and a variety of slice thicknesses, noise levels, and levels of intensity non-uniformity. These data are available for viewing in three orthogonal views (transversal, sagittal, and coronal), and for downloading.

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. BODB offers a way to document computational models of brain function by linking each model to Brain Operating Principles (BOPs), related brain regions, Summaries of Simulation Results (SSRs)and Summaries of Experimental Data (SEDs) used either to design or to test the model. Tools are provided to search for related models and to compare their coverage of SEDs. This allows automatic benchmarking of a model against a cluster of models addressing similar BOPs or SEDs or brain regions. Tools allow display of brain imaging results against a human brain applet; a new tool will link data to a macaque brain applet.

A database that contains brain imaging data collected on 3T MRI scanners from over 200 normally developing healthy children from birth to 18 years. The imaging data stored in the C-MIND database are DTI, HARDI, 3DT1W, 3DT2W, concurrent ASL-BOLD scans during two language tasks (Stories and Sentence-Picture Matching), Resting State fMRI and Baseline ASL scans.

Fluorodeoxyglucose Positron Emission Tomography (FDG-PET) is currently one of the powerful tools for the clinical diagnosis of dementia such as Alzheimer's Disease (AD). Meanwhile, MR imaging, being non-radioactive and having high contrast resolution, is highly accessible in clinical settings. Therefore, this dataset intends to use FDG-PET images as the Ground Truth for evaluating AD, for the development of predicting AD patients using MR images. This dataset includes an AD group and a control group (Healthy Group). The determination of the image diagnosis group is made by neurology specialists based on comprehensive judgment using clinically relevant information. Each set of data contains one set of MRI T1 images and one set of FDG-PET images. The image format is DICOM, and all images have been anonymized. To obtain the clinical information and related documentation, please contact the administrator.

Comprehensive three-dimensional digital atlas database of the C57BL/6J mouse brain based on magnetic resonance microscopy images acquired on a 17.6-T superconducting magnet. This database consists of: Individual MRI images of mouse brains; three types of atlases: individual atlases, minimum deformation atlases and probabilistic atlases; the associated quantitative structural information, such as structural volumes and surface areas. Quantitative group information, such as variations in structural volume, surface area, magnetic resonance microscopy image intensity and local geometry, have been computed and stored as an integral part of the database. The database augments ongoing efforts with other high priority strains as defined by the Mouse Phenome Database focused on providing a quantitative framework for accurate mapping of functional, genetic and protein expression patterns acquired by a myriad of technologies and imaging modalities. You must register First (Mandatory) and then you may Download Images and Data.

Atlas of magnetic resonance images and histological sections of a Japanese monkey brain, Rhesus monkey and human. The Brain Explorer allows for display, magnification, and comparison these images. Other formats include a collection of .jpg images, Quicktime VR (allow user to zoom in), and EmonV, a voxel viewer for MacOS X.

A database to support research on drugs for the treatment of different neurological disorders. It contains agents that act on neuronal receptors and signal transduction pathways in the normal brain and in nervous disorders. It enables searches for drug actions at the level of key molecular constituents, cell compartments and individual cells, with links to models of these actions.

Collection of neuroanatomically labeled MRI brain scans, created by neuroanatomical experts. Regions of interest include the sub-cortical structures (thalamus, caudate, putamen, hippocampus, etc), along with ventricles, brain stem, cerebellum, and gray and white matter and sub-divided cortex into parcellation units that are defined by gyral and sulcal landmarks.

THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 21, 2017.Database developed for storing, retrieving and cross-referencing neuroscience information about the connectivity of the avian brain. It contains entries about the new and old terminology of the areas and their hierarchy and data on connections between brain regions, as well as a functional keyword system linked to brain regions and connections.

Project Description

Hyperspectral imaging and machine learning have been employed in the medical field for classifying highly infiltrative brain tumors. Although existing HSI databases of in-vivo human brains are available, they present two main deficiencies. Firstly, the amount of labeled data is scarce and secondly, 3D-tissue information is unavailable. To address both issues, we present the SLIMBRAIN database, a multimodal image database of in-vivo human brains which provides HS brain tissue data within the 400-1000 nm spectrum, as well as RGB, depth and multi-view images. Two HS cameras, two depth cameras and different RGB sensors were used to capture images and videos from 193 patients. All data in the SLIMBRAIN database can be used in a variety of ways, for example to train ML models with more than 1 million HS pixels available and labeled by neurosurgeons, to reconstruct 3D scenes or to visualize RGB brain images with different pathologies, offering unprecedented flexibility for both the medical and engineering communities.

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Data Description

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The SLIMBRAIN database contains anonymous hyperspectral, depth and RGB image data from in-vivo, and also ex-vivo, human brains from 193 patients.

SLIMBRAIN database. The available data are:

- CalibrationFiles: 5 .zip files to calibrate hyperspectral data for the different SLIMBRAIN prototypes and 1 .zip file containing the intrinsic and extrinsic parameters for some cameras.

- Datasets: 2 .zip files containing the patient's datasets for the snapshot and linescan hyperspectral cameras.

- GroundTruthMaps: 2 .zip files containing the patient's ground-truths folders for the snapshot and linescan hyperspectral cameras.

- PaperExperiments: 1 .zip files containing several files that store the patient IDs used for the results shown in the paper.

- preProcessedImages: Several .zip files containing the hyperspectral pre-processed cubes for the snapshot and linescan hyperspectral cameras.

- RawFiles: 193 .zip files containing the raw files acquired in the operating room for each of the 193 patients. These files contains the raw images from different cameras, videos and depth images.

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Notes

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To access the SLIMBRAIN Database, you need to fill, accept and sign the Data Usage Agreement terms. Then, you need to send it to us, using the emails included at the end of the document. We will evaluate your application and, if you are accepted, you will receive a confirmation email with the necessary steps to access the data.

You can either find the Data Usage Agreement within this page or at https://slimbrain.citsem.upm.es. Then, you could access https://slimbrain.citsem.upm.es/search to filter the patients using the available online service provided by Research Center on Software Technologies and Multimedia Systems for Sustainability (CITSEM) and Fundación para la Investigación Biomédica del Hospital Universitario 12 de Octubre (FIBH12O).

You could also use https://slimbrain.citsem.upm.es/files to see the raw data online without the need of downloading it.

For further information, you can visit the official SLIMBRAIN database website at https://slimbrain.citsem.upm.es, where you can find Python software to manage the hyperspectral data provided.

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Files

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- CalibrationFiles:

These files store the calibration files necessary for the hyperspectral data and depth cameras.

Specifically, folders starting with a number indicate a hyperspectral calibration library with dark

and white references at different working distances and tilt angles:

- 1_Tripod_popoman: For the Ximea snapshot camera. Illumination done with the Dolan Jenner lamp and ambient fluorescent lamps turned on. Obtained in the operating room when empty.

- 2_Prototype_laser: For the Ximea snapshot camera. Illumination done with the Dolan Jenner lamp and ambient fluorescent lamps turned on. Obtained in the operating room when empty.

- 3_Protoype_lidar: For the Ximea snapshot and Headwall linescan cameras. Illumination done with the Dolan Jenner lamp and ambient fluorescent lamps turned on. Obtained in the operating room when empty.

- 4_Prototype_lidar: For the Ximea snapshot and Headwall linescan cameras. Illumination done with the Osram lamp and ambient fluorescent lamps turned on. Obtained in the operating room when empty.

- 5_Prototype_Kinect: For the Ximea snapshot and Headwall linescan cameras. Illumination done with the International Light lamp and ambient fluorescent lamps turned off. Obtained in the laboratory.

Furthermore, the depth, RGB and HS sensor calibration files, including intrinsic, extrinsic and distortion

parameters, are included as .json files in DepthCameraCalibrationFiles.

- Datasets:

These files stores each patient dataset with the spectral information of every labelled pixel. These are obtained from the coordinates of its corresponding ground-truth map and pre-processed cube, which have been labeled by the neurosurgeons using a labelling tool based on the Spectral Angle Map (SAM) metric. Patient datasets are available for the Ximea snapshot and Headwall linescan hyperspectral cameras.

- GroundTruthMaps:

These files stores each patient ground-truth map labeled by the neurosurgeons. The labelling tool is based on the Spectral Angle Map (SAM) metric as already used in existing hyperspectral in-vivo human brain databases. Patient ground-truth maps are available for the Ximea snapshot and Headwall linescan hyperspectral cameras.

- PaperExperiments.zip:

Contains 2 .txt files with the patient's IDs used for the experiments shown in the paper.

- preProcessedImages:

These files stores each patient hyperspectral pre-processed cube. These are obtained from the raw data included in the RawFiles folder and the described pre-processing chain applied to them. Patient pre-processed cubes are available for the Ximea snapshot and Headwall linescan hyperspectral cameras.

- RawFiles:

These files stores the raw files obtained in each of the operations. It can include hyperspectral data, RGB data and depth information for each patient ID. All data is anonimized to keep the privacy of each human patient.

BossDB (Brain Observatory Storage Service and Database) is a cloud-based ecosystem for the storage and management of public large-scale volumetric neuroimaging and connectomics datasets. This includes volumetric Electron Microscopy and X-Ray Micro/Nanotomography data with support for multi-channel image data, segmentations, annotations, meshes, and connectomes. BossDB integrates with community resources for data access, processing, visualization, and analysis, and includes an API that enables metadata management, rendering, datatype conversions, and ingest.

We report on MRi-Share, a multi-modal brain MRI database acquired in a unique sample of 1,870 young healthy adults, aged 18 to 35 years, while undergoing university-level education. MRi-Share contains structural (T1 and FLAIR), diffusion (multispectral), susceptibility weighted (SWI), and resting-state functional imaging modalities. Here, we described the contents of these different neuroimaging datasets and the processing pipelines used to derive brain phenotypes, as well as how quality control was assessed. In addition, we present preliminary results on associations of some of these brain image-derived phenotypes at the whole brain level with both age and sex, in the subsample of 1,722 individuals aged less than 26 years. We demonstrate that the post-adolescence period is characterized by changes in both structural and microstructural brain phenotypes. Grey matter cortical thickness, surface area and volume were found to decrease with age, while white matter volume shows increase. Diffusivity, either radial or axial, was found to robustly decrease with age whereas fractional anisotropy only slightly increased. As for the neurite orientation dispersion and densities, both were found to increase with age. The isotropic volume fraction also showed a slight increase with age. These preliminary findings emphasize the complexity of changes in brain structure and function occurring in this critical period at the interface of late maturation and early aging.

The HIV Brain Sequence Database (HIVBrainSeqDB) is a public database of HIV envelope sequences, directly sequenced from brain and other tissues from the same patients. For inclusion in the database, sequences must: (i) be deposited in Genbank; (ii) include some portion of the HIV env region; (iii) be clonal, amplified directly from tissue; and (iv) be sampled from the brain, or sampled from a patient for which the database already contains brain sequence. Sequences are annotated with clinical data including viral load, CD4 count, antiretroviral status, neurocognitive impairment, and neuropathological diagnosis, all curated from the original publication. Tissue source is coded using an anatomical ontology, the Foundational Model of Anatomy, to capture the maximum level of detail available, while maintaining ontological relationships between tissues and their subparts. 44 tissue types are represented within the database, grouped into 4 categories: (i) brain, brainstem, and spinal cord; (ii) meninges, choroid plexus, and CSF; (iii) blood and lymphoid; and (iv) other (bone marrow, colon, lung, liver, etc). Currently, the database contains 2517 envelope sequences from 90 patients, obtained from 22 published studies. 1272 sequences are from brain; the remaining 1245 are from blood, lymph node, spleen, bone marrow, colon, lung and other non-brain tissues. The database interface utilizes a faceted interface, allowing real-time combination of multiple search parameters to assemble a meta-dataset, which can be downloaded for further analysis. This online resource will greatly facilitate analysis of the genetic aspects of HIV macrophage tropism, HIV compartmentalization and evolution within the brain and other tissue reservoirs, and the relationship of these findings to HIV-associated neurological disorders and other clinical consequences of HIV infection.

Brain-Computer Interfaces, and especially passive Brain-Computer Interfaces (pBCI), with their ability to estimate and detect mental states, are receiving increasing attention from both the scientific and the research and development communities. Many pBCIs aim to increase the safety of complex work environments such as in the aeronautical domain. Therefore, mental workload, vigilance and decision-making are some of the most commonly examined aspects of cognition within this field of research. A large proportion of pBCIs involve a component of machine learning and signal processing as the data that are collected need to be transformed into a reliable estimate of the users’ current mental state (e.g. mental workload). Improving this component is a major challenge for researchers, requiring large quantities of data. While data sharing is common for the active BCI community, open pBCI datasets are scarcer and generally incomplete with regards to the information they report. This is particularly true for datasets encompassing several tasks or sessions, which are of importance for tackling the challenges of transfer learning. Testing new pipelines, feature extraction algorithms and classifiers are central issues for future advances in research within this domain, as well as for algorithm benchmark and research reproducibility.The COG-BCI database presented here is comprised of the recordings of 29 participants over 3 individual sessions with 4 different tasks designed to elicit different cognitive states. This results in a total of over 100 hours of open electrophysiological (EEG) and electrocardiogram (ECG) data. The project was validated by the local ethical committee of the University of Toulouse (CER number 2021-342). The dataset was validated on a subjective, behavioral and physiological level (i.e. cardiac and cerebral activity), to ensure its usefulness to the pBCI community. This body of work represents a large effort to promote the use of pBCIs, as well as the use of open science.

The data are in the Brain Imaging Data Structure (BIDS) format. For more information, please read the COG-BCI_info.pdf file.

A platform that allow users to visualize and analyze transcriptome data related to the genetics that underlie the development, function, and dysfunction stages and states of the brain. Users can search for cerebellar development genes by name, ID, keyword, expression, and tissue specificity. Search results include general information, links, temporal, spatial, and tissue information, and gene category.

A database of brain neuroanatomic volumetric observations spanning various species, diagnoses, and structures for both individual and group results. A major thrust effort is to enable electronic access to the results that exist in the published literature. Currently, there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the dissemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies, as well as metaanalysis. Extensions that permit pre-published, non-published and other representation are planned, again to facilitate comparative analyses. Design strategy: The principle organizing data structure is the "publication". Publications report on "groups" of subjects. These groups have "demographic" information as well as "volume" information for the group as a whole. Groups are comprised of "individuals", which also have demographic and volume information for each of the individuals. The finest-grained data structure is the "individual volume record" which contains a volume observation, the units for the observation, and a pointer to the demographic record for individual upon which the observation is derived. A collection of individual volumes can be grouped into a "group volume" observation; the group can be demographically characterized by the distribution of individual demographic observations for the members of the group.

Preliminary database of neuroanatomical connectivity reports specifically for the human brain, which have been manually curated. It includes details (based on manual literature curation) of tract tracing or related connectivity studies conducted in human brain tissue. This database and user interface will be expanded and improved in the near future.

The Brain/MINDS Marmoset MRI NA216 and eNA91 datasets currently constitutes the largest public marmoset brain MRI resource (483 individuals), and includes in vivo and ex vivo data for large variety of image modalities covering a wide age range of marmoset subjects.
* The in vivo part corresponds to a total of 455 individuals, ranging in age from 0.6 to 12.7 years (mean age: 3.86 ± 2.63), and standard brain data (NA216) from 216 of these individuals (mean age: 4.46 ± 2.62).
T1WI, T2WI, T1WI/T2WI, DTI metrics (FA, FAc, MD, RD, AD), DWI, rs-fMRI in awake and anesthetized states, NIfTI files (.nii.gz) of label data, individual brain and population average connectome matrix (structural and functional) csv files are included.
* The ex vivo part is ex vivo data, mainly from a subset of 91 individuals with a mean age of 5.27 ± 2.39 years.
It includes NIfTI files (.nii.gz) of standard brain, T2WI, DTI metrics (FA, FAc, MD, RD, AD), DWI, and label data, and csv files of individual brain and population average structural connectome matrices.

This database contains information on protein expression in the Drosophila melanogaster brain. It consists of a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project. Currently there are 884 brain scans from 535 protein trap lines in the database. Drosophila protein trap strains were generated by the St Johnston Lab and the Russell Lab at the University of Cambridge, UK. The piggyBac insertion method was used to insert constructs containing splice acceptor and donor sites, StrepII and FLAG affinity purification tags, and an EYFP exon (Venus). Brain images were acquired by Seymour Knowles-Barley, in the Armstrong Lab at the University of Edinburgh. Whole brain mounts were imaged by confocal microscopy, with a background immunohistochemical label added to aid the identification of brain structures. Additional immunohistochemical labeling of the EYFP protein using an anti-GFP antibody was also used in most cases. The trapped protein signal (EYFP / anti-GFP), background signal (NC82 label), and the merged signal can be viewed on the website by using the corresponding channel buttons. In all images the trapped protein / EYFP signal appears green and the background / NC82 channel appears magenta. Original .lsm image files are also available for download.

Please refer to readme.txt file